more quality of life updates

arhdf.log

@@ -1,51 +0,0 @@
-
-=== Channel: Adhesion:Retrace ===
-  DimScaling shape:   (2, 2)
-  DimScaling[0,:]:    [8.656250e-06 1.665625e-05]  (row 0)
-  DimScaling[1,:]:    [-4.e-06  4.e-06]  (row 1)
-  --- If [start, end] interpretation ---
-    xreal (row1 range) = 8e-06
-    yreal (row0 range) = 7.999999999999998e-06
-  --- If [step, offset] interpretation ---
-    row0: step=8.656249999999648e-06  offset=1.6656249999999646e-05
-    row1: step=-4e-06  offset=4e-06
-  DimUnits:           ['m' 'm']
-  DataUnits:          N
-  DimExtents ('Resolution 0'): [512 384]
-
-=== Channel: FFMZSensor:Retrace ===
-  DimScaling shape:   (2, 2)
-  DimScaling[0,:]:    [8.656250e-06 1.665625e-05]  (row 0)
-  DimScaling[1,:]:    [-4.e-06  4.e-06]  (row 1)
-  --- If [start, end] interpretation ---
-    xreal (row1 range) = 8e-06
-    yreal (row0 range) = 7.999999999999998e-06
-  --- If [step, offset] interpretation ---
-    row0: step=8.656249999999648e-06  offset=1.6656249999999646e-05
-    row1: step=-4e-06  offset=4e-06
-  DimUnits:           ['m' 'm']
-  DataUnits:          m
-  DimExtents ('Resolution 0'): [512 384]
-
-=== Channel: MaxForce:Retrace ===
-  DimScaling shape:   (2, 2)
-  DimScaling[0,:]:    [8.656250e-06 1.665625e-05]  (row 0)
-  DimScaling[1,:]:    [-4.e-06  4.e-06]  (row 1)
-  --- If [start, end] interpretation ---
-    xreal (row1 range) = 8e-06
-    yreal (row0 range) = 7.999999999999998e-06
-  --- If [step, offset] interpretation ---
-    row0: step=8.656249999999648e-06  offset=1.6656249999999646e-05
-    row1: step=-4e-06  offset=4e-06
-  DimUnits:           ['m' 'm']
-  DataUnits:          N
-  DimExtents ('Resolution 0'): [512 384]
-
-=== 2D dataset shapes ===
-  Image/DataSet/Resolution 0/Frame 0/Adhesion:Retrace/Image  shape=(512, 384)
-  Image/DataSet/Resolution 0/Frame 0/FFMZSensor:Retrace/Image  shape=(512, 384)
-  Image/DataSet/Resolution 0/Frame 0/MaxForce:Retrace/Image  shape=(512, 384)
-  Image/DataSetInfo/Global/Channels/Adhesion:Retrace/Thumbnail  shape=(128, 128)
-  Image/DataSetInfo/Global/Channels/FFMZSensor:Retrace/Thumbnail  shape=(128, 128)
-  Image/DataSetInfo/Global/Channels/MaxForce:Retrace/Thumbnail  shape=(128, 128)
-  Image/DataSetInfo/Global/Thumbnail  shape=(128, 128)

backend/nodes/mask_threshold.py

@@ -23,7 +23,7 @@ class ThresholdMask:
 
     OUTPUTS = (
         ('IMAGE', 'mask'),
-        ('RECORD_TABLE', 'threshold'),
+        ('FLOAT', 'threshold'),
     )
     FUNCTION = "process"
 

backend/server.py

@@ -60,6 +60,22 @@ FRONTEND_DIR = frontend_dir()
 DIST_DIR = frontend_dist_dir()
 PNG_SIGNATURE = b"\x89PNG\r\n\x1a\n"
 
+GITHUB_REPO = "vipqualitypost/tono"
+_APP_VERSION: str | None = None
+
+
+def _get_app_version() -> str:
+    global _APP_VERSION
+    if _APP_VERSION is not None:
+        return _APP_VERSION
+    try:
+        import tomllib
+        with open(project_root() / "pyproject.toml", "rb") as f:
+            _APP_VERSION = tomllib.load(f)["project"]["version"]
+    except Exception:
+        _APP_VERSION = "0.0.0"
+    return _APP_VERSION
+
 
 class _SafeEncoder(json.JSONEncoder):
     def default(self, obj):
@@ -568,6 +584,30 @@ def create_app(
             )
         return ws
 
+    async def check_update(_request: web.Request) -> web.Response:
+        import aiohttp as _aiohttp
+
+        current = _get_app_version()
+        url = f"https://api.github.com/repos/{GITHUB_REPO}/releases/latest"
+        try:
+            async with _aiohttp.ClientSession() as session:
+                async with session.get(url, timeout=_aiohttp.ClientTimeout(total=5),
+                                       headers={"Accept": "application/vnd.github.v3+json"}) as resp:
+                    if resp.status != 200:
+                        return web.json_response({"current": current, "latest": None, "update_available": False})
+                    data = await resp.json()
+            latest = str(data.get("tag_name", "")).lstrip("vV")
+            html_url = str(data.get("html_url", ""))
+            update_available = latest != "" and latest != current
+            return web.json_response({
+                "current": current,
+                "latest": latest,
+                "update_available": update_available,
+                "url": html_url,
+            })
+        except Exception:
+            return web.json_response({"current": current, "latest": None, "update_available": False})
+
     app = web.Application()
     app["allow_local_filesystem"] = allow_local_filesystem
 
@@ -587,6 +627,7 @@ def create_app(
     app.router.add_get("/help-docs", get_help_docs)
     app.router.add_get("/help-docs/{filename}", get_help_doc_file)
     app.router.add_post("/prompt", submit_prompt)
+    app.router.add_get("/check-update", check_update)
     app.router.add_get("/ws", websocket_handler)
 
     if (DIST_DIR / "assets").exists():

docs/nodes/3D View.md

@@ -26,7 +26,7 @@ Interactive 3D surface view of a DATA_FIELD. Use the mesh input for geometry and
 | resolution | INT | 128 | Downsampling resolution for mesh generation (32–512) |
 | make_solid | BOOLEAN | False | When enabled adds a flat base and side walls to close the mesh |
 
-## Limitations
+## Notes
 
 - Resolution is applied by uniform subsampling; fine features smaller than one mesh step may be lost.
 - Non-square pixels emit a warning and the 3D surface represents physical scan area, not pixel grid.

docs/nodes/ACF 1D.md

@@ -21,7 +21,7 @@ Compute the one-dimensional autocorrelation function of a line profile. Only pos
 |------|------|---------|-------------|
 | level | dropdown | mean | Pre-processing: subtract mean before correlation, or none |
 
-## Limitations
+## Notes
 
 - Only one-sided (positive lag) ACF is returned.
 - Peak period detection finds only the first local maximum; multi-periodic signals report only the shortest detected period.

docs/nodes/ACF 2D.md

@@ -20,7 +20,7 @@ Compute the two-dimensional autocorrelation function with Gwyddion-style mean or
 |------|------|---------|-------------|
 | level | dropdown | mean | Pre-processing applied before correlation: mean subtraction, plane subtraction, or none |
 
-## Limitations
+## Notes
 
 - Output is not normalized to [−1, 1]; peak value equals the field variance.
 - Plane levelling assumes a linear trend; strongly curved surfaces may not detrend correctly.

docs/nodes/Angle Measure.md

@@ -22,7 +22,7 @@ Measure the included angle between two draggable line segments over a DATA_FIELD
 | color | STRING (color picker) | #ff9800 | Overlay color for the angle arms and arc |
 | stroke_width | FLOAT | 1.35 | Line thickness in display pixels (0.35–6.0) |
 
-## Limitations
+## Notes
 
 - Coordinates are stored as fractions of the image dimensions; physical units depend on the input field's calibration.
 - Angle measurement is the included angle at the vertex, always in [0°, 180°].

docs/nodes/Annotations.md

@@ -25,6 +25,6 @@ Attach optional publication-style annotations (scale bar, color-map legend) to a
 | show_color_map | BOOLEAN | True | Render a color-map legend with min/mid/max values |
 | text_size | FLOAT | 14.0 | Font size in points for annotation labels (6–96) |
 
-## Limitations
+## Notes
 
 - Scale bar and color-map legend require the input to carry physical dimension and unit metadata; plain images without metadata will emit a warning and the feature will be skipped.

docs/nodes/Blind Tip Estimate.md

@@ -24,7 +24,7 @@ Blind tip estimation from a measured SPM image using the Villarrubia algorithm.
 | method | dropdown | partial | partial: uses local maxima only (faster, needs sharp isolated features); full: uses all points above morphological opening (slower, more robust) |
 | use_edges | BOOLEAN | False | When enabled, also uses image edge pixels as refinement candidates |
 
-## Limitations
+## Notes
 
 - Requires sharp, isolated features on the surface for reliable results.
 - Output tip has the same pixel size as the input field; tip deconvolution requires matching pixel sizes.

docs/nodes/Color Map.md

@@ -20,7 +20,7 @@ None.
 | preset | dropdown | viridis | Built-in colormap preset name; visible when mode is preset |
 | stops | STRING (colormap editor) | default gradient | JSON array of color stops for the custom gradient; visible when mode is custom |
 
-## Limitations
+## Notes
 
 - Custom colormaps must include at least a minimum and maximum color stop.
 - Stops must be valid JSON; invalid JSON will raise an error.

docs/nodes/Colormap Adjust.md

@@ -22,7 +22,7 @@ Adjust how a DATA_FIELD maps into its colormap without changing the underlying d
 | scale | FLOAT | 1.0 | Zoom the colormap range (0.05–4.0); values below 1 stretch contrast |
 | auto | BUTTON | — | Reset offset to 0 and scale to 1 (full data range) |
 
-## Limitations
+## Notes
 
 - Only the display mapping metadata is changed; raw data values are unaffected.
 - Scale must be positive and finite; zero or negative values raise an error.

docs/nodes/Coordinate Pair.md

@@ -19,6 +19,6 @@ Combine two COORD values into a single COORDPAIR for use with nodes that accept
 
 None.
 
-## Limitations
+## Notes
 
 - Coordinates are expected to be in the [0, 1] fractional range; values outside this range may produce unexpected results in downstream nodes.

docs/nodes/Coordinate.md

@@ -19,6 +19,6 @@ None.
 | x | FLOAT | 0.5 | Horizontal position as a fraction of image width (0 = left, 1 = right) |
 | y | FLOAT | 0.5 | Vertical position as a fraction of image height (0 = top, 1 = bottom) |
 
-## Limitations
+## Notes
 
 - Values are clamped to [0, 1] by downstream nodes; this node does not enforce clamping itself.

docs/nodes/Crop-Resize.md

@@ -24,7 +24,7 @@ Crop a DATA_FIELD with a draggable rectangle defined by two corners, then option
 | target_height | INT | 0 | Output pixel height after resampling (0 = keep cropped height) |
 | interpolation | dropdown | bilinear | Resampling interpolation: bilinear, nearest, or bicubic |
 
-## Limitations
+## Notes
 
 - The crop region must have non-zero width and height; an error is raised otherwise.
 - If only one of target_width or target_height is set, the other dimension is computed to preserve aspect ratio.

docs/nodes/Cross Section.md

@@ -23,7 +23,7 @@ Extract a cross-section height profile along a line between two draggable points
 | extend | dropdown | none | none: profile between the two markers; to_edges: extend line to image borders |
 | n_samples | INT | 0 | Number of sample points along the profile (0 = auto, one per pixel diagonal) |
 
-## Limitations
+## Notes
 
 - Profile is sampled using cubic spline interpolation (order 3); sharp step edges may show ringing.
 - Physical x-axis of the output profile is the Euclidean distance in field xy units.

docs/nodes/Cross-Correlate.md

@@ -22,7 +22,7 @@ Compute 2D cross-correlation between two fields. The correlation peak indicates
 | mode | dropdown | same | Output size: full (Na+Nb−1), same (same as field_a), or valid (overlapping region only) |
 | normalize | BOOLEAN | True | Normalize the result to [−1, 1] by dividing by the product of RMS values |
 
-## Limitations
+## Notes
 
 - Both fields must be of compatible numpy array types; very different sizes in full mode produce large outputs.
 - Mean is subtracted before correlation; absolute offset information is lost.

docs/nodes/Cursors.md

@@ -20,7 +20,7 @@ Place two draggable cursors on a line plot or 2D field to measure positions and
 
 None (cursor positions are set by dragging in the preview panel).
 
-## Limitations
+## Notes
 
 - When a COORDPAIR is connected, the cursor positions are locked and cannot be dragged interactively.
 - On 2D fields, z values are sampled with bilinear (order 1) interpolation.

docs/nodes/Curvature.md

@@ -24,7 +24,7 @@ Fit a quadratic surface and report the overall principal curvature radii and dir
 |------|------|---------|-------------|
 | masking | dropdown | ignore | How to use the mask: ignore (fit all pixels), include (fit only masked pixels), or exclude (fit unmasked pixels) |
 
-## Limitations
+## Notes
 
 - Requires at least six usable pixels for the quadratic fit; fewer pixels produce no output.
 - The fit assumes a globally smooth quadratic surface; locally rough or step-like surfaces give unreliable results.

docs/nodes/Custom Convolution.md

@@ -22,7 +22,7 @@ Apply a user-defined convolution kernel to a DATA_FIELD. Enter rows of space-sep
 | normalize | BOOLEAN | True | Divide the result by the sum of absolute kernel values to preserve amplitude |
 | boundary | dropdown | reflect | Boundary handling: reflect, nearest, or wrap |
 
-## Limitations
+## Notes
 
 - Kernel must be a rectangle: all rows must have the same number of values.
 - Maximum kernel size is 51×51; larger kernels are rejected.

docs/nodes/Draw Mask.md

@@ -22,7 +22,7 @@ Paint a binary mask directly over an image preview. Pen size controls newly draw
 | invert | BOOLEAN | False | When enabled, swaps painted and unpainted regions |
 | clear_mask | BUTTON | — | Clears all painted strokes |
 
-## Limitations
+## Notes
 
 - Strokes are stored as path data; very long painting sessions with many strokes may accumulate large state.
 - The mask resolution matches the input field resolution and cannot be changed independently.

docs/nodes/Edge Detect.md

@@ -21,7 +21,7 @@ Detect edges using Sobel, Prewitt, Laplacian, or Laplacian-of-Gaussian (LoG) ope
 | method | dropdown | sobel | Edge detection operator: sobel, prewitt, laplacian, or log (Laplacian of Gaussian) |
 | sigma | FLOAT | 1.0 | Gaussian smoothing sigma used only for the LoG operator (0.1–10.0) |
 
-## Limitations
+## Notes
 
 - sigma is ignored for sobel, prewitt, and laplacian methods.
 - Sobel and Prewitt return gradient magnitude; Laplacian and LoG return signed second-derivative values.

docs/nodes/Entropy.md

@@ -22,7 +22,7 @@ Compute the Shannon entropy of the height or slope distribution. H = −Σ p·ln
 | mode | dropdown | height values | Compute entropy of height values or slope magnitude |
 | n_bins | INT | 256 | Number of histogram bins for probability estimation (16–1024) |
 
-## Limitations
+## Notes
 
 - Entropy is sensitive to n_bins; very few bins underestimate entropy while very many bins overestimate it for small fields.
 - Non-finite pixel values are removed before binning.

docs/nodes/FFT 1D.md

@@ -19,7 +19,7 @@ Compute the FFT amplitude spectrum of a line profile and identify the dominant p
 
 None.
 
-## Limitations
+## Notes
 
 - The DC component is excluded from the output.
 - Spectrum is one-sided (real FFT); the x-axis shows period, not frequency.

docs/nodes/FFT 2D.md

@@ -24,7 +24,7 @@ Compute the 2D FFT with optional windowing and mean/plane subtraction. Outputs l
 | windowing | dropdown | hann | Window function applied before FFT: hann, hamming, blackman, or none |
 | level | dropdown | mean | Pre-processing: subtract mean, subtract plane, or none |
 
-## Limitations
+## Notes
 
 - Output fields are in the frequency domain; physical units on axes are spatial frequency (1/m).
 - Phase output uses the raw FFT phase and is sensitive to field origin; it is most useful when paired with the Inverse 2D FFT node.

docs/nodes/FFT Filter.md

@@ -23,7 +23,7 @@ Frequency-domain filtering of a line profile or 2D data field using a Butterwort
 | cutoff_high | FLOAT | 0.4 | Upper cutoff for bandpass/notch modes (0.001–1.0) |
 | order | INT | 2 | Butterworth filter order; higher values give steeper roll-off (1–10) |
 
-## Limitations
+## Notes
 
 - cutoff_high is only used for bandpass and notch modes.
 - The filter is applied in the frequency domain via FFT; very short lines may show wrap-around artefacts.

docs/nodes/Facet Level.md

@@ -21,7 +21,7 @@ Level a field by iteratively finding the dominant local facet orientation and su
 |------|------|---------|-------------|
 | masking | dropdown | exclude | How to use the mask: exclude (ignore masked facets), include (use only masked facets), or ignore (use all facets) |
 
-## Limitations
+## Notes
 
 - Requires compatible XY and Z physical units for correct facet gradient estimation.
 - Needs at least four valid facet cells; fields smaller than 2×2 pixels are not processed.

docs/nodes/Field Arithmetic.md

@@ -21,7 +21,7 @@ Apply a point-wise arithmetic operation to two DATA_FIELDs of the same resolutio
 |------|------|---------|-------------|
 | operation | dropdown | add | Element-wise operation: add, subtract, multiply, divide, min, max, or hypot (√(a²+b²)) |
 
-## Limitations
+## Notes
 
 - Both fields must have exactly the same pixel dimensions; mismatched sizes raise an error.
 - divide may produce NaN or Inf pixels where field_b is zero.

docs/nodes/Fix Zero.md

@@ -20,6 +20,6 @@ Shift data so that the minimum, mean, or median value becomes zero. Equivalent t
 |------|------|---------|-------------|
 | method | dropdown | min | Reference value to set to zero: min (lowest pixel), mean (average), or median |
 
-## Limitations
+## Notes
 
 - None.

docs/nodes/Flip.md

@@ -20,6 +20,6 @@ Reflect a DATA_FIELD across the X axis (top/bottom) or Y axis (left/right). Phys
 |------|------|---------|-------------|
 | axis | dropdown | x | Flip axis: x flips top/bottom (vertical mirror), y flips left/right (horizontal mirror) |
 
-## Limitations
+## Notes
 
 - None.

docs/nodes/Float Slider.md

@@ -20,6 +20,6 @@ None.
 | max_value | FLOAT | 1.0 | Upper bound of the slider range |
 | value | FLOAT (slider) | 0.5 | Current value within [min_value, max_value] |
 
-## Limitations
+## Notes
 
 - None.

docs/nodes/Folder.md

@@ -18,7 +18,7 @@ None.
 |------|------|---------|-------------|
 | folder | FOLDER_PICKER | "" | Path to the folder to list |
 
-## Limitations
+## Notes
 
 - Only files with supported extensions are listed; subdirectories and unsupported file types are ignored.
 - The number of file output sockets is determined at load time by the folder contents.

docs/nodes/Font.md

@@ -19,7 +19,7 @@ None.
 | family | dropdown | System default | Font family name; includes discovered system fonts plus "Custom file" option |
 | font_file | FILE_PICKER | "" | Path to a custom font file; visible only when family is set to "Custom file" |
 
-## Limitations
+## Notes
 
 - Custom font files must be in a format supported by the underlying font rendering library (e.g. TTF, OTF).
 - System fonts are enumerated at startup; newly installed fonts require restarting the application.

docs/nodes/Fractal Dimension.md

@@ -21,7 +21,7 @@ Calculate the surface fractal dimension using Gwyddion's partitioning, cube coun
 | method | dropdown | partitioning | Algorithm: partitioning, cube_counting, triangulation, psdf (power spectrum), or hhcf (structure function) |
 | interpolation | dropdown | linear | Interpolation used when resampling the field to a square grid: linear, nearest, or cubic |
 
-## Limitations
+## Notes
 
 - The field is resampled to a square grid internally; highly anisotropic scan sizes may introduce interpolation artefacts.
 - Fit range can be adjusted interactively on the log-log plot; the default range covers the full data.

docs/nodes/Gaussian Filter.md

@@ -20,7 +20,7 @@ Apply a Gaussian blur to a DATA_FIELD. Equivalent to gwy_data_field_filter_gauss
 |------|------|---------|-------------|
 | sigma | FLOAT | 1.0 | Standard deviation of the Gaussian kernel in pixels (0.01–50.0) |
 
-## Limitations
+## Notes
 
 - sigma is specified in pixels, not physical units; the effective physical blur depends on pixel size.
 - Large sigma values (> ~20 pixels) are slow due to the large kernel.

docs/nodes/Gradient.md

@@ -20,7 +20,7 @@ Compute the spatial gradient using a Sobel operator. Outputs the gradient magnit
 |------|------|---------|-------------|
 | component | dropdown | magnitude | Output component: magnitude (√(gx²+gy²)), x (horizontal gradient), y (vertical gradient), or azimuth (angle in degrees) |
 
-## Limitations
+## Notes
 
 - Gradient components are in units of z_unit/xy_unit; azimuth is in degrees.
 - Sobel operator uses a 3×3 kernel; sub-pixel features smaller than one pixel cannot be resolved.

docs/nodes/Grain Analysis.md

@@ -21,7 +21,7 @@ Label connected grain regions in a binary mask and compute per-grain statistics:
 |------|------|---------|-------------|
 | min_size | INT | 10 | Minimum grain area in pixels; smaller connected regions are ignored (1–100000) |
 
-## Limitations
+## Notes
 
 - Grain detection uses 2D connected-component labeling on the binary mask; the field and mask must have the same pixel dimensions.
 - Physical area and diameter values require the field to carry valid physical calibration (xreal, yreal, si_unit_xy).

docs/nodes/Grain Distance Transform.md

@@ -23,7 +23,7 @@ Compute the mask distance transform using Gwyddion-style interior, exterior, or
 | output_type | dropdown | interior | Output mode: interior (distances inside grains), exterior (distances outside), or signed (positive inside, negative outside) |
 | from_border | BOOLEAN | True | When enabled, image borders are treated as mask boundaries |
 
-## Limitations
+## Notes
 
 - Output distances are in physical xy units derived from the field calibration.
 - The mask must have the same pixel dimensions as the field.

docs/nodes/Grain Filter.md

@@ -22,7 +22,7 @@ Remove grains from a binary mask based on size and border contact. Equivalent to
 | max_area | INT | 0 | Discard grains with more pixels than this value (0 = no upper limit) |
 | remove_border | BOOLEAN | False | Discard any grain that touches the image edge |
 
-## Limitations
+## Notes
 
 - Grain detection uses 4-connected or 8-connected labeling; the exact connectivity is determined by the implementation.
 - min_area and max_area are in pixels, not physical units.

docs/nodes/Histogram.md

@@ -22,7 +22,7 @@ Compute the height distribution histogram (DH). Use log scale to reveal small pe
 | n_bins | INT | 256 | Number of histogram bins (10–1000) |
 | y_scale | dropdown | linear | Y-axis scale: linear or log |
 
-## Limitations
+## Notes
 
 - Cursor positions are stored as fractions of the histogram range and are set interactively.
 - Log scale displays bins as log(count); bins with zero count appear as the minimum log value.

docs/nodes/Image (Demo).md

@@ -19,7 +19,7 @@ None.
 | name | dropdown | (first demo file) | Name of the bundled demo file to load |
 | colormap | dropdown | viridis | Colormap applied to the field; hidden when colormap_map is connected |
 
-## Limitations
+## Notes
 
 - Only files present in the bundled demo directory are available; custom files cannot be added here.
 - If no demo files are found, the dropdown shows "(no demo files found)".

docs/nodes/Image.md

@@ -22,7 +22,7 @@ Load any supported file. SPM formats (.gwy, .sxm, .ibw) and HDF5 (.h5, .hdf5) pr
 | filename | FILE_PICKER | "" | Path to the file to load; hidden when path input is connected |
 | colormap | dropdown | viridis | Colormap applied to the loaded field; hidden when colormap_map is connected |
 
-## Limitations
+## Notes
 
 - Uncalibrated formats (images, arrays) emit a warning and produce fields without physical dimensions.
 - Multi-channel files (e.g. .gwy with multiple data channels) produce one DATA_FIELD output socket per channel; the socket count is determined at load time.

docs/nodes/Inverse 2D FFT.md

@@ -21,7 +21,7 @@ Reconstruct a spatial-domain image from a 2D frequency spectrum. For exact recon
 |------|------|---------|-------------|
 | representation | dropdown | magnitude | How to interpret the spectrum input: magnitude, log_magnitude, or psdf |
 
-## Limitations
+## Notes
 
 - The spectrum input must be a frequency-domain DATA_FIELD; connecting a spatial-domain field raises an error.
 - If phase is connected, it must also be a frequency-domain field with the same shape as the spectrum.

docs/nodes/Kuwahara Filter.md

@@ -20,7 +20,7 @@ Edge-preserving smoothing using Kuwahara's minimum-variance quadrant method. Unl
 |------|------|---------|-------------|
 | iterations | INT | 1 | Number of times the 5×5 Kuwahara pass is applied (1–20) |
 
-## Limitations
+## Notes
 
 - The kernel is fixed at 5×5 pixels; coarser smoothing requires more iterations.
 - Multiple iterations increase processing time proportionally; 20 iterations on a large field may be slow.

docs/nodes/Line Correction.md

@@ -27,7 +27,7 @@ Correct scan-line mismatches using Gwyddion-derived row alignment methods. Suppo
 | trim_fraction | FLOAT | 0.05 | Fraction of extreme values to trim; visible only for trimmed_mean and trimmed_diff methods (0–0.5) |
 | polynomial_degree | INT | 1 | Polynomial degree for the polynomial method (0–5); visible only for polynomial method |
 
-## Limitations
+## Notes
 
 - The step method is designed for step-like scan artifacts and may over-correct smooth surfaces.
 - Mask shape must match the field shape if a mask is connected.

docs/nodes/Local Contrast.md

@@ -21,7 +21,7 @@ Expand the local dynamic range at each pixel to reveal fine surface features tha
 | kernel_size | INT | 10 | Size of the local neighbourhood window in pixels (2–100) |
 | weight | FLOAT | 0.5 | Blend weight between original and full-contrast output (0 = original, 1 = full local contrast; 0–1) |
 
-## Limitations
+## Notes
 
 - Large kernel sizes are slow; values above ~50 pixels may be noticeably slow on large fields.
 - The enhancement is purely a display-contrast operation; it changes the underlying data values.

docs/nodes/Markup.md

@@ -23,7 +23,7 @@ Draw simple vector shapes (lines, rectangles, circles, arrows) over a DATA_FIELD
 | stroke_width | INT | 3 | Line thickness in display pixels for newly drawn shapes (1–64) |
 | clear_shapes | BUTTON | — | Remove all drawn shapes |
 
-## Limitations
+## Notes
 
 - Shapes are stored as fractional coordinates; physical positions depend on field calibration.
 - Individual shape properties (color, width) cannot be changed after drawing; use Clear Shapes to start over.

docs/nodes/Mask Invert.md

@@ -19,6 +19,6 @@ Invert a binary mask — swap masked and unmasked regions.
 
 None.
 
-## Limitations
+## Notes
 
 - None.

docs/nodes/Mask Morphology.md

@@ -23,6 +23,6 @@ Apply morphological operations to a binary mask. Dilate expands regions, erode s
 | radius | INT | 1 | Structuring element radius in pixels (1–50) |
 | shape | dropdown | disk | Structuring element shape: disk or square |
 
-## Limitations
+## Notes
 
 - Large radius values (> ~20 pixels) may be slow on large masks.

docs/nodes/Mask Operations.md

@@ -21,6 +21,6 @@ Apply boolean logic to two binary masks. Supports AND, OR, XOR, NAND, NOR, XNOR,
 |------|------|---------|-------------|
 | operation | dropdown | and | Boolean operation: and, or, xor, xnor, nand, nor, a_minus_b, b_minus_a, a, b, not_a, not_b, a_implies_b, b_implies_a, false, true |
 
-## Limitations
+## Notes
 
 - Both masks must have the same pixel dimensions.

docs/nodes/Median Filter.md

@@ -20,7 +20,7 @@ Apply a median filter to a DATA_FIELD. Equivalent to gwy_data_field_filter_media
 |------|------|---------|-------------|
 | size | INT | 3 | Kernel size (side length) in pixels; odd values only (1–21) |
 
-## Limitations
+## Notes
 
 - The median filter is applied with a square kernel; non-square (e.g. rectangular) kernels are not supported.
 - Large kernel sizes are significantly slower than the Gaussian filter for the same smoothing extent.

docs/nodes/Note.md

@@ -20,7 +20,7 @@ Read the Note metadata from an .ibw (Igor binary wave) file and display all entr
 |------|------|---------|-------------|
 | filename | FILE_PICKER | "" | Path to the .ibw file; hidden when path input is connected |
 
-## Limitations
+## Notes
 
 - Only .ibw files are supported; other formats raise an error.
 - If the .ibw note section is empty or missing, an error is raised.

docs/nodes/Number.md

@@ -18,6 +18,6 @@ None.
 |------|------|---------|-------------|
 | value | FLOAT | 0.0 | The numeric value to output |
 
-## Limitations
+## Notes
 
 - None.

docs/nodes/PSDF.md

@@ -21,7 +21,7 @@ Compute the two-dimensional power spectral density function with Gwyddion-style
 | windowing | dropdown | hann | Window function applied before FFT to reduce spectral leakage: hann, hamming, blackman, or none |
 | level | dropdown | mean | Pre-processing: subtract mean, subtract plane, or none |
 
-## Limitations
+## Notes
 
 - Output is in the frequency domain; physical units on axes are spatial frequency (1/m) and PSDF units are z_unit²·m².
 - Window RMS compensation is applied to normalize the spectral density consistently across window choices.

docs/nodes/Plane Level.md

@@ -21,6 +21,6 @@ Fit and subtract a least-squares plane from the data. Supports include/exclude m
 |------|------|---------|-------------|
 | masking | dropdown | ignore | How to use the mask: ignore (use all pixels), include (fit plane to masked pixels only), or exclude (exclude masked pixels from fit) |
 
-## Limitations
+## Notes
 
 - When masking is include or exclude, the unmasked/masked region must contain at least three non-collinear pixels to fit a plane.

docs/nodes/Polynomial Level.md

@@ -22,7 +22,7 @@ Fit and subtract a polynomial background of given degree in x and y. Equivalent
 | degree_x | INT | 2 | Polynomial degree in the x direction (0–5) |
 | degree_y | INT | 2 | Polynomial degree in the y direction (0–5) |
 
-## Limitations
+## Notes
 
 - High polynomial degrees (> 4) may overfit and introduce artificial long-range modulation.
 - No masking support; all pixels contribute equally to the fit.

docs/nodes/Preview.md

@@ -19,7 +19,7 @@ None.
 |------|------|---------|-------------|
 | colormap | dropdown | auto | Colormap used when rendering a DATA_FIELD or grayscale IMAGE; hidden when colormap_map is connected |
 
-## Limitations
+## Notes
 
 - When no input is connected, an error is raised at execution time.
 - Connecting a FILE_PATH socket (instead of DATA_FIELD) raises a type error; ensure the correct socket is connected.

docs/nodes/Print Table.md

@@ -16,6 +16,6 @@ None.
 
 None.
 
-## Limitations
+## Notes
 
 - None.

docs/nodes/Radial Profile.md

@@ -22,7 +22,7 @@ Compute the azimuthally averaged radial profile from a centre point. The output
 | cy | FLOAT | 0.5 | Centre y position as a fraction of field height (0 = top, 1 = bottom) |
 | n_bins | INT | 128 | Number of radial bins (4–4096) |
 
-## Limitations
+## Notes
 
 - Pixels are assigned to radial bins by Euclidean distance; bins near the centre contain fewer pixels and may be noisier.
 - Physical x-axis units come from the field's si_unit_xy; uncalibrated fields produce pixel-unit radii.

docs/nodes/Resample.md

@@ -22,7 +22,7 @@ Resample a DATA_FIELD to a new pixel resolution while preserving physical dimens
 | height | INT | 256 | Output pixel height (2–16384) |
 | interpolation | dropdown | linear | Interpolation method: linear, cubic, or nearest |
 
-## Limitations
+## Notes
 
 - Physical dimensions are preserved; upsampling does not add new information.
 - Very large output sizes (e.g. 16384×16384) require substantial memory.

docs/nodes/Rotate.md

@@ -22,7 +22,7 @@ Rotate a DATA_FIELD counterclockwise by an angle in degrees. Optionally expand t
 | interpolation | dropdown | bilinear | Interpolation method for resampling: bilinear, nearest, or bicubic |
 | expand_canvas | BOOLEAN | True | When True, canvas is expanded to contain the full rotated image; when False, canvas is clipped to original size |
 
-## Limitations
+## Notes
 
 - Rotation by angles other than multiples of 90° introduces interpolation artefacts.
 - expand_canvas may produce fields with non-square pixel sizes for arbitrary angles.

docs/nodes/Save Layers.md

@@ -22,7 +22,7 @@ None.
 | format | dropdown | TIFF | Output format: TIFF (multi-page, float32 for fields) or NPZ (named arrays) |
 | layer_name_0 … layer_name_N | STRING | "" | Optional name for each layer; used as TIFF page descriptions or NPZ array keys |
 
-## Limitations
+## Notes
 
 - At least one layer must be connected; an error is raised otherwise.
 - TIFF writes DATA_FIELD layers as float32; IMAGE layers are written as uint8.

docs/nodes/Save.md

@@ -22,7 +22,7 @@ None.
 | format | STRING (context-dependent) | TIFF | Output format; available choices depend on the connected input type |
 | plot_title | STRING | "" | Optional title for line plots saved as PNG or TIFF |
 
-## Limitations
+## Notes
 
 - Available formats per input type: DATA_FIELD → TIFF, PNG, NPZ; IMAGE → PNG, TIFF, NPZ; LINE → PNG, TIFF, CSV, NPZ, JSON; RECORD_TABLE/DATA_TABLE → CSV, JSON; FLOAT → TXT, JSON; MESH_MODEL → OBJ, STL.
 - divide-by-zero or NaN values in fields are preserved in TIFF/NPZ but may not render correctly in PNG.

docs/nodes/Scar Removal.md

@@ -25,7 +25,7 @@ Detect and remove horizontal scan scars using Gwyddion-derived scar marking thre
 | min_length | INT | 16 | Minimum horizontal run length in pixels to classify as a scar (1–4096) |
 | max_width | INT | 4 | Maximum vertical width in pixels for a scar candidate (1–32) |
 
-## Limitations
+## Notes
 
 - Designed for horizontal (fast-scan) scars only; vertical scars are not detected.
 - Aggressive thresholds may remove legitimate surface features that resemble scars.

docs/nodes/Slope Distribution.md

@@ -21,7 +21,7 @@ Compute the angular slope distribution of a DATA_FIELD surface. Equivalent to Gw
 | distribution | dropdown | theta | Distribution type: theta (inclination angle, probability density in 1/deg), phi (azimuthal direction, weighted by slope², 0–360°), or gradient (slope magnitude, probability density in 1/(z/xy)) |
 | n_bins | INT | 90 | Number of histogram bins (10–1000) |
 
-## Limitations
+## Notes
 
 - The gradient magnitude distribution requires valid physical xy and z units for correct normalization.
 - phi distribution is weighted by slope squared; flat surfaces with near-zero slopes produce a noisy azimuthal distribution.

docs/nodes/Spot Removal.md

@@ -22,7 +22,7 @@ Fill defect pixels (hot pixels, dropouts, scan artifacts) by interpolation. The
 | method | dropdown | laplace | Inpainting method: laplace (smooth Laplace equation solution), mean (local mean), or zero |
 | max_iter | INT | 100 | Maximum number of iterations for the Laplace solver (1–2000) |
 
-## Limitations
+## Notes
 
 - Large masked regions may not converge fully within max_iter iterations using the Laplace method.
 - The mean method uses a simple neighbourhood average and may leave visible discontinuities at large defect clusters.

docs/nodes/Statistics.md

@@ -18,6 +18,6 @@ Compute basic surface statistics: min, max, mean, RMS roughness, median, and ske
 
 None.
 
-## Limitations
+## Notes
 
 - None.

docs/nodes/Stats.md

@@ -21,7 +21,7 @@ Compute a contextual scalar statistic from a LINE, record table, DATA_FIELD, or
 | operation | STRING (context-dependent dropdown) | mean | Statistical operation; available choices depend on the input type |
 | column | STRING | value | Column name for DATA_TABLE inputs; visible only when a DATA_TABLE is connected |
 
-## Limitations
+## Notes
 
 - Available operations vary by input type; connecting a different type changes the available options.
 - For DATA_TABLE inputs, the column must match an existing column name; an error is raised otherwise.

docs/nodes/Template Match.md

@@ -22,7 +22,7 @@ Find a template pattern within a larger data field using normalised cross-correl
 |------|------|---------|-------------|
 | threshold | FLOAT | 0.8 | Minimum correlation score to mark as a detection (0.0–1.0) |
 
-## Limitations
+## Notes
 
 - The template must be smaller than the image; equal or larger sizes are not supported.
 - Normalized cross-correlation assumes uniform background; strong global gradients reduce detection accuracy.

docs/nodes/Text Note.md

@@ -17,6 +17,6 @@ None.
 | text | STRING (multiline) | "# Guide\n\nDouble-click to edit this note.\n\n- Step 1\n- Step 2" | Markdown text displayed on the canvas card |
 | color | dropdown | default | Card background color: default, blue, green, yellow, red, or purple |
 
-## Limitations
+## Notes
 
 - None.

docs/nodes/Threshold Mask.md

@@ -23,7 +23,7 @@ Create a binary mask by thresholding data. Otsu automatically finds the optimal
 | threshold | FLOAT | 0.0 | Threshold value; for absolute: raw z value; for relative: fraction 0–1; ignored for otsu (socket-only input) |
 | direction | dropdown | above | Which pixels to select: above or below the threshold |
 
-## Limitations
+## Notes
 
 - For the relative method, the threshold fraction is applied to the full data range [min, max].
 - Otsu thresholding may not give meaningful results on non-bimodal height distributions.

docs/nodes/Tip Deconvolution.md

@@ -19,7 +19,7 @@ Reconstruct the true surface from a tip-broadened measured AFM image. Uses morph
 
 None.
 
-## Limitations
+## Notes
 
 - The tip pixel size must match the image pixel size exactly; mismatched calibrations will produce incorrect results.
 - Deconvolution can only reduce tip broadening; it cannot recover information lost below the noise floor.

docs/nodes/Tip Model.md

@@ -23,7 +23,7 @@ Generate a synthetic AFM tip model DATA_FIELD. The input field sets the pixel si
 | half_angle | FLOAT | 20.0 | Half-cone angle from the tip axis in degrees for the cone shape (1–89°) |
 | n_pixels | INT | 65 | Side length of the square tip grid in pixels (odd values only, 3–511) |
 
-## Limitations
+## Notes
 
 - half_angle is only used for the cone shape.
 - The tip grid must be smaller than or equal to the image size for Tip Deconvolution to work correctly.

docs/nodes/Value Display.md

@@ -21,7 +21,7 @@ Display a FLOAT value, or a selected numeric row from a measurement table, and p
 | number_input | STRING (text input) | "0" | Manual numeric entry, e.g. "1.5 nm"; hidden when value socket is connected |
 | measurement | STRING (dropdown) | "" | Row selector when a RECORD_TABLE is connected; visible only for RECORD_TABLE inputs |
 
-## Limitations
+## Notes
 
 - When a RECORD_TABLE is connected, only rows with numeric values can be selected; non-numeric rows are not accessible.
 - Manual text entry supports optional SI unit suffix (e.g. "1.5 nm") for display only; the output FLOAT is always the raw numeric value.

docs/nodes/Watershed Segmentation.md

@@ -27,7 +27,7 @@ Segment a height field into grains using the two-stage Gwyddion watershed workfl
 | watershed_drop_size | FLOAT | 0.1 | Relative drop size for watershed growth stage (0.0001–1.0) |
 | combine_mode | dropdown | replace | How to combine with an existing mask: replace (ignore existing), union (OR), or intersection (AND) |
 
-## Limitations
+## Notes
 
 - Parameter tuning is required; the default settings work best for isolated round features.
 - Very large locate_threshold values may reject all seeds and produce an empty mask.

docs/nodes/Wavelet Denoise.md

@@ -23,7 +23,7 @@ Denoise a DATA_FIELD using wavelet coefficient thresholding. BayesShrink adapts
 | sigma | FLOAT | 0.0 | Noise level estimate in data units; 0 = automatic estimation (0–1.0) |
 | mode | dropdown | soft | Thresholding mode: soft (smooth shrinkage) or hard (zero below threshold) |
 
-## Limitations
+## Notes
 
 - The field size should ideally be a power of two for best wavelet decomposition; other sizes are handled by padding.
 - sigma = 0 triggers automatic noise estimation from the finest-scale wavelet coefficients; this may be inaccurate on strongly structured surfaces.

frontend/src/App.tsx

@@ -3001,6 +3001,13 @@ function Flow() {
     return () => document.removeEventListener('pointerdown', handler);
   }, [menuOpen]);
 
+  // Auto-dismiss status toast after 5 seconds
+  useEffect(() => {
+    if (!status.text) return;
+    const timer = setTimeout(() => setStatus({ text: '', level: 'info' }), 5000);
+    return () => clearTimeout(timer);
+  }, [status]);
+
   useEffect(() => {
     const handler = (e: KeyboardEvent) => {
       if ((e.ctrlKey || e.metaKey) && e.key === 'Enter') {

frontend/src/HelpPanelManager.tsx

@@ -2,6 +2,18 @@ import React, { useEffect, useMemo, useRef, useState } from 'react';
 import ReactDOM from 'react-dom';
 import { marked } from 'marked';
 
+// Open external links in new tabs
+const renderer = new marked.Renderer();
+const defaultLinkRenderer = renderer.link.bind(renderer);
+renderer.link = function (token) {
+  const html = defaultLinkRenderer(token);
+  if (token.href && /^https?:\/\//.test(token.href)) {
+    return html.replace(/^<a /, '<a target="_blank" rel="noopener noreferrer" ');
+  }
+  return html;
+};
+marked.use({ renderer });
+
 interface Heading {
   level: number;
   text: string;

frontend/src/styles.css

@@ -154,7 +154,7 @@ html, body, #root {
 .floating-menu-toggle {
   width: 40px;
   height: 40px;
-  border-radius: 10px;
+  border-radius: 20px;
   border: 1px solid var(--border-toolbar);
   background: var(--bg-toolbar);
   cursor: pointer;
@@ -170,8 +170,8 @@ html, body, #root {
 }
 
 .floating-menu-logo {
-  width: 28px;
+  width: 40px;
-  height: 28px;
+  height: 40px;
   border-radius: 6px;
 }
 
@@ -744,6 +744,9 @@ html, body, #root {
 
 .node-help-panel-body strong { color: #e2e8f0; }
 
+.node-help-panel-body a { color: #ff9800; }
+.node-help-panel-body a:hover { color: #ffb74d; }
+
 /* ── Help panel TOC + content layout ──────────────────────────────── */
 
 .help-content-row {